Abstract
BackgroundFor decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms.ResultsHere we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (Salmo salar) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment.ConclusionsThe INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.
Highlights
Linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance
INDEL discovery from expressed sequence tags (ESTs) Clustering of 431,073 Atlantic salmon ESTs resulted in 185,615 singletons and 34,311 contigs with an average size 1,072 bp
AutoSNP identified 6,189 INDELs which corresponds to the average INDEL density of one indel per 5,948 bp (1.68 × 104 per bp)
Summary
Linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. Inexpensive, simple and flexible genotyping solutions that enable rapid screening of hundreds to thousands of individuals for intermediate numbers of loci (~75-300) would be extremely useful for QTL mapping applications in a broad range of organisms. Such a need is still inadequately met with currently available open-source and commercial genotyping platforms as they require expensive, highly specific laboratory equipment (e.g. array-based SNP genotyping platforms) and/or suffer high initial costs because of the use of long (SNPWaveTM,) or modified primers (e.g. TaqMan, SNP-SCALE) [9,10]
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